In article <170708590S86.SBROWN at GAES.GRIFFIN.PEACHNET.EDU>,
SBROWN at GAES.GRIFFIN.PEACHNET.EDU (Stuart Brown) wrote:
> We have had to deal with the same problem in our core lab. I have found the
> ABI software totally inadequate for sequence assembly and far too time
> consuming for even routine file management of sequences. We have been using
> "Sequencher" from Gene Codes Co. (Ann Arbor, MI) which works fairly well.
> The nicest feature of this program is automatic vector removal. For short
> inserts where you get vector at the 3' end, you can totally ignore the bad
> sequence at the end of the run. For large inserts we usually truncate the
> seq. either automatically at 500 bp, or wherever the "NNN's" start to appear.
> After using the assemble functions and putting together the contigs, we can
> then restore the crummy 3' end sequence to help editing ambiguities. There is
> just no point trying to use bad sequence to assemble contigs.
>
We like Sequencher quite well (we pitched the ABI SeqEd program). The new
version due out early next year is supposed to bring some intelligence to
deleting back 3'and 5'end sequences based on readability of the sequence.
Unfortunately I don't think ABI or GeneCodes is planning on giving us
confidence limits for base calls anytime soon that would allow really good
automatic truncation. In Sequencher the truncated sequence is not deleted
from a project, just suppressed, so it's easy to get back if you need it.
--
Thanks,
Roger
mailto::rcwieg at ccmail.monsanto.com